Figure 1. The 3D-Zernike Descriptor Extraction Process. A given protein surface is extracted and voxelized into a cubic grid. The following step involves the 3D-Zernike transformation into a vector of descriptors (121 numbers).

Computational proteomics approaches for rational drug design

Software and hardware used in the research

x86_64 Intel(R) Core(TM)2 CPU 6400 @ 2.13GHz GNU/Linux

Condor

3D Zernike Descriptor program

Project Director : Assistant Professor Daisuke Kihara

Department of Biological Sciences/Computer Science

Tel: 765-496-2284

Email: dkihara@purdue.edu

Contact information

Purdue

University

Project Summery

Rapidly accumulating genome sequence data and protein tertiary structures, together with recent advance of bioinformatics techniques open a new way of computational systematic drug discovery. In the post-genomic era, utilizing established knowledge of protein structure function relationship in bioinformatics field is a promising strategy for cost-effective rational drug development. Our project is focused on development computational methods for comparing ligand binding sites and ligand binding sites with ligands. The methods we will develop can effectively capture similarity and dissimilarity of geometrical and physicochemical features of local protein 3D surfaces. We employ projection-based method, 3D Zernike Descriptor, to enable fast comparison.